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Stinson LF, Ma J, Lai CT, Rea A, Perrella SL, Geddes DT. Milk microbiome transplantation: recolonizing donor milk with mother's own milk microbiota. Appl Microbiol Biotechnol 2024; 108:74. [PMID: 38194146 PMCID: PMC10776751 DOI: 10.1007/s00253-023-12965-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/29/2023] [Accepted: 12/10/2023] [Indexed: 01/10/2024]
Abstract
Donor human milk (DHM) provides myriad nutritional and immunological benefits for preterm and low birthweight infants. However, pasteurization leaves DHM devoid of potentially beneficial milk microbiota. In the present study, we performed milk microbiome transplantation from freshly collected mother's own milk (MOM) into pasteurized DHM. Small volumes of MOM (5%, 10%, or 30% v/v) were inoculated into pasteurized DHM and incubated at 37 °C for up to 8 h. Further, we compared microbiome recolonization in UV-C-treated and Holder-pasteurized DHM, as UV-C treatment has been shown to conserve important biochemical components of DHM that are lost during Holder pasteurization. Bacterial culture and viability-coupled metataxonomic sequencing were employed to assess the effectiveness of milk microbiome transplantation. Growth of transplanted MOM bacteria occurred rapidly in recolonized DHM samples; however, a greater level of growth was observed in Holder-pasteurized DHM compared to UV-C-treated DHM, potentially due to the conserved antimicrobial properties in UV-C-treated DHM. Viability-coupled metataxonomic analysis demonstrated similarity between recolonized DHM samples and fresh MOM samples, suggesting that the milk microbiome can be successfully transplanted into pasteurized DHM. These results highlight the potential of MOM microbiota transplantation to restore the microbial composition of UV-C-treated and Holder-pasteurized DHM and enhance the nutritional and immunological benefits of DHM for preterm and vulnerable infants. KEY POINTS: • Mother's own milk microbiome can be successfully transplanted into donor human milk. • Recolonization is equally successful in UV-C-treated and Holder-pasteurized milk. • Recolonization time should be restricted due to rapid bacterial growth.
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Affiliation(s)
- Lisa F Stinson
- School of Molecular Sciences, The University of Western Australia, Perth, Australia.
| | - Jie Ma
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | - Ching Tat Lai
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | - Alethea Rea
- Mathematics and Statistics, Murdoch University, Perth, Australia
| | - Sharon L Perrella
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | - Donna T Geddes
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
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2
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Ingram K, Gregg C, Tegge A, Elison JT, Lin W, Howell BR. Metagenomic assessment of the bacterial breastfeeding microbiome in mature milk across lactation. Front Pediatr 2024; 11:1275436. [PMID: 39092171 PMCID: PMC11292495 DOI: 10.3389/fped.2023.1275436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/25/2023] [Indexed: 08/04/2024] Open
Abstract
Introduction Research has illustrated the presence of a diverse range of microbiota in human milk. The composition of the milk microbiome varies across different stages of lactation, emphasizing the need to consider the lactation stage when studying its composition. Additionally, the transfer of both milk and skin microbiota during breastfeeding is crucial for understanding their collective impact on infant health and development. Further exploration of the complete breastfeeding microbiome is necessary to unravel the role these organisms play in infant development. We aim to longitudinally assess the bacterial breastfeeding microbiome across stages of lactation. This includes all the bacteria that infants are exposed to during breastfeeding, such as bacteria found within human milk and any bacteria found on the breast and nipple. Methods Forty-six human milk samples were collected from 15 women at 1, 4, 7, and 10 months postpartum. Metagenomic analysis of the bacterial microbiome for these samples was performed by CosmosID (Rockville, MD) via deep sequencing. Results Staphylococcus epidermidis and Propionibacteriaceae species are the most abundant bacterial species from these samples. Samples collected at 10 months showed higher abundances of Proteobacteria, Streptococcaceae, Lactobacillales, Streptococcus, and Neisseria mucosa compared to other timepoints. Alpha diversity varied greatly between participants but did not change significantly over time. Discussion As the bacterial breastfeeding microbiome continues to be studied, bacterial contributions could be used to predict and reduce health risks, optimize infant outcomes, and design effective management strategies, such as altering the maternal flora, to mitigate adverse health concerns.
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Affiliation(s)
- Kelly Ingram
- Virginia Tech Carilion School of Medicine, Roanoke, VA, United States
| | - Collin Gregg
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, VA, United States
| | - Allison Tegge
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, VA, United States
| | - Jed T. Elison
- Institute for Child Development, University of Minnesota, Minneapolis, MN, United States
- Masonic Institute for the Developing Brain, University of Minnesota, St. Paul, MN, United States
| | - Weili Lin
- Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Brittany R. Howell
- Virginia Tech Carilion School of Medicine, Roanoke, VA, United States
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, VA, United States
- Department of Human Development and Family Science, Virginia Tech, Blacksburg, VA, United States
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3
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Brockway M. The role of antibiotic exposure and the effects of breastmilk and human milk feeding on the developing infant gut microbiome. Front Public Health 2024; 12:1408246. [PMID: 38903564 PMCID: PMC11187292 DOI: 10.3389/fpubh.2024.1408246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/28/2024] [Indexed: 06/22/2024] Open
Abstract
The World Health Organization (WHO) recommends exclusive breastfeeding for the first 6 months of life followed by complementary foods and sustained breastfeeding for at least 2 years, underscoring its pivotal role in reducing infant mortality and preventing various illnesses. This perspective delves into the intricate relationship between breastfeeding practices, early life antibiotic exposure, and infant gut microbiome development, highlighting their profound influence on child health outcomes. Antibiotics are extensively prescribed during pregnancy and childhood, disrupting the microbiome, and are related to increased risks of allergies, obesity, and neurodevelopmental disorders. Breastfeeding is a significant determinant of a healthier gut microbiome, characterized by higher levels of beneficial bacteria such as Bifidobacterium and lower levels of potential pathogens. Despite widespread recognition of the benefits of breastfeeding, gaps persist in healthcare practices and support mechanisms, exacerbating challenges faced by breastfeeding families. This highlights the pressing need for comprehensive research encompassing breastfeeding behaviors, human milk intake, and their impact on infant health outcomes. Additionally, promoting awareness among healthcare providers and families regarding the detrimental effects of unnecessary formula supplementation could facilitate informed decision-making and bolster exclusive breastfeeding rates. Moreover, donor human milk (DHM) is a promising alternative to formula, potentially mitigating disruptions to the infant gut microbiome after antibiotic exposure. Overall, prioritizing breastfeeding support interventions and bridging research gaps are essential steps towards improving child health outcomes on a global scale.
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Affiliation(s)
- Meredith Brockway
- Faculty of Nursing, University of Calgary, Calgary, AB, Canada
- Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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4
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Stinson LF, George A, Gridneva Z, Jin X, Lai CT, Geddes DT. Effects of Different Thawing and Warming Processes on Human Milk Composition. J Nutr 2024; 154:314-324. [PMID: 38042352 DOI: 10.1016/j.tjnut.2023.11.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 11/22/2023] [Accepted: 11/29/2023] [Indexed: 12/04/2023] Open
Abstract
The composition of human milk is influenced by storage and processing practices. The effects of thawing and warming practices on human milk composition remain poorly studied despite their prevalence in home, research, and donor milk bank settings. This review comprehensively examines the impact of different thawing and warming methods on nutritional and bioactive human milk components. While some components such as carbohydrates and minerals remain stable under most typical thawing and warming conditions, others, such as fat, immune proteins, bacterial and human cells, and peptide amine hormones, are sensitive to warming. This review has identified that the data on the effects of milk thawing and warming is limited and often contradictory. Given that numerous important components of milk are diminished during cold storage, it is important that thawing and warming practices do not lead to further loss of or alterations to beneficial milk components. Further work in this field will facilitate greater standardization of thawing methods among researchers and underpin recommendations for thawing and warming of expressed milk for parents.
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Affiliation(s)
- Lisa F Stinson
- School of Molecular Sciences, The University of Western Australia, Perth, Australia.
| | - Alexandra George
- Metabolomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, Australia
| | - Zoya Gridneva
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | - Xuehua Jin
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | - Ching Tat Lai
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | - Donna T Geddes
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
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5
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Briere CE, Gomez J. Fresh Parent's Own Milk for Preterm Infants: Barriers and Future Opportunities. Nutrients 2024; 16:362. [PMID: 38337647 PMCID: PMC10857054 DOI: 10.3390/nu16030362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/19/2024] [Accepted: 01/20/2024] [Indexed: 02/12/2024] Open
Abstract
While direct at-the-breast feeding is biologically optimal, Neonatal Intensive Care Unit (NICU) admission due to infant immaturity or illness often necessitates the expression and storage of parent's milk. The provision of freshly expressed (never stored) parent's own milk to preterm infants is not widely prioritized, and this article provides an exploration of NICU practices and their implications for feeding premature or ill infants with parent's own milk. In this article, we discuss the potential biological benefits of fresh parent's own milk, highlighting its dynamic components and the changes incurred during storage. Research suggests that fresh milk may offer health advantages over stored milk. The authors advocate for further research, emphasizing the need for standardized definitions. Research is needed on the biological impact of fresh milk, both short- and long-term, as well as defining and understanding healthcare economics when using fresh milk.
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Affiliation(s)
- Carrie-Ellen Briere
- Elaine Marieb College of Nursing, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Institute of Nursing Research and Evidence-Based Practice, Connecticut Children’s, Hartford, CT 06106, USA
| | - Jessica Gomez
- Department of Pediatrics/Neonatal-Perinatal Medicine, McGovern School of Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA;
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6
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Spreckels JE, Fernández-Pato A, Kruk M, Kurilshikov A, Garmaeva S, Sinha T, Ghosh H, Harmsen H, Fu J, Gacesa R, Zhernakova A. Analysis of microbial composition and sharing in low-biomass human milk samples: a comparison of DNA isolation and sequencing techniques. ISME COMMUNICATIONS 2023; 3:116. [PMID: 37945978 PMCID: PMC10636111 DOI: 10.1038/s43705-023-00325-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/18/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
Human milk microbiome studies are currently hindered by low milk bacterial/human cell ratios and often rely on 16S rRNA gene sequencing, which limits downstream analyses. Here, we aimed to find a method to study milk bacteria and assess bacterial sharing between maternal and infant microbiota. We tested four DNA isolation methods, two bacterial enrichment methods and three sequencing methods on mock communities, milk samples and negative controls. Of the four DNA isolation kits, the DNeasy PowerSoil Pro (PS) and MagMAX Total Nucleic Acid Isolation (MX) kits provided consistent 16S rRNA gene sequencing results with low contamination. Neither enrichment method substantially decreased the human metagenomic sequencing read-depth. Long-read 16S-ITS-23S rRNA gene sequencing biased the mock community composition but provided consistent results for milk samples, with little contamination. In contrast to 16S rRNA gene sequencing, 16S-ITS-23S rRNA gene sequencing of milk, infant oral, infant faecal and maternal faecal DNA from 14 mother-infant pairs provided sufficient resolution to detect significantly more frequent sharing of bacteria between related pairs compared to unrelated pairs. In conclusion, PS or MX kit-DNA isolation followed by 16S rRNA gene sequencing reliably characterises human milk microbiota, and 16S-ITS-23S rRNA gene sequencing enables studies of bacterial transmission in low-biomass samples.
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Grants
- This study was supported by funds from the Dutch Research Council (NWO-VIDI grant 016.178.056 to A.Z., NWO-VICI grant VI.C.202.022 to J.F., NWO gravitation grant Exposome-NL 024.004.017 to A.K. and A.Z., NWO gravitation grant Netherlands Organ-on-Chip Initiative 024.003.001 to J.F.), the Dutch Heart Foundation (IN-CONTROL CVON2018-27 to J.F.), the European Research Council (ERC starting grant 715772 to A.Z., ERC consolidator grant 101001678 to J.F.), an EASI-Genomics grant (PID7780 to T.S. and A.Z.), the De-Cock Hadders foundation (2021-57 to J.E.S., 2021-08 to S.G.), the International Society for Research in Human Milk and Lactation (ISRHML, personal grant to J.E.S), the Winston Bakker Fonds (WB-08, granted to T.S.), and the European Union’s Horizon 2020 research innovation program (824110). S.G. and T.S. hold scholarships from the Graduate School of Medical Sciences and the Junior Scientific Masterclass of the University of Groningen, the Netherlands, respectively. The Lifelines NEXT cohort study received funds from the University Medical Center Groningen Hereditary Metabolic Diseases Fund, Health~Holland (Top Sector Life Sciences and Health), the Ubbo Emmius Foundation, the European Union, the Northern Netherlands Alliance (SNN), the provinces of Friesland and Groningen, the municipality of Groningen, Philips, and the Société des Produits Nestlé.
- De-Cock Hadders foundation (2021-57) International Society of Research in Human Milk and Lactation (ISRHML personal grant)
- Dutch Research Council (NWO gravitation grant Exposome-NL 024.004.017)
- De-Cock Hadders foundation (2021-08) University of Groningen Graduate School of Medical Sciences (scholarship)
- EASI-Genomics (grant PID7780) Winston Bakker Fonds (WB-08) University of Groningen Junior Scientific Masterclass (scholarship)
- Dutch Research Council (NWO-VICI grant VI.C.202.022) Dutch Research Council (NWO gravitation grant Netherlands Organ-on-Chip Initiative 024.003.001) European Research Council (ERC consolidator grant 101001678)
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Affiliation(s)
- Johanne E Spreckels
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Asier Fernández-Pato
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Marloes Kruk
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Sanzhima Garmaeva
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Trishla Sinha
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Hiren Ghosh
- Medical Center - University of Freiburg, Institute for Infection Prevention and Hospital Epidemiology, Freiburg, Germany
| | - Hermie Harmsen
- Department of Medical Microbiology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
- Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Ranko Gacesa
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands.
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Coates LC, Durham SD, Storms DH, Magnuson AD, Van Hekken DL, Plumier BM, Finley JW, Fukagawa NK, Tomasula PM, Lemay DG, Picklo MJ, Barile D, Kalscheur KF, Kable ME. Associations among Milk Microbiota, Milk Fatty Acids, Milk Glycans, and Inflammation from Lactating Holstein Cows. Microbiol Spectr 2023; 11:e0402022. [PMID: 37074179 PMCID: PMC10269560 DOI: 10.1128/spectrum.04020-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 03/23/2023] [Indexed: 04/20/2023] Open
Abstract
Milk oligosaccharides (MOs) can be prebiotic and antiadhesive, while fatty acids (MFAs) can be antimicrobial. Both have been associated with milk microbes or mammary gland inflammation in humans. Relationships between these milk components and milk microbes or inflammation have not been determined for cows and could help elucidate a novel approach for the dairy industry to promote desired milk microbial composition for improvement of milk quality and reduction of milk waste. We aimed to determine relationships among milk microbiota, MFAs, MOs, lactose, and somatic cell counts (SCC) from Holstein cows, using our previously published data. Raw milk samples were collected at three time points, ranging from early to late lactation. Data were analyzed using linear mixed-effects modeling and repeated-measures correlation. Unsaturated MFA and short-chain MFA had mostly negative relationships with potentially pathogenic genera, including Corynebacterium, Pseudomonas, and an unknown Enterobacteriaceae genus but numerous positive relationships with symbionts Bifidobacterium and Bacteroides. Conversely, many MOs were positively correlated with potentially pathogenic genera (e.g., Corynebacterium, Enterococcus, and Pseudomonas), and numerous MOs were negatively correlated with the symbiont Bifidobacterium. The neutral, nonfucosylated MO composed of eight hexoses had a positive relationship with SCC, while lactose had a negative relationship with SCC. One interpretation of these trends might be that in milk, MFAs disrupt primarily pathogenic bacterial cells, causing a relative increase in abundance of beneficial microbial taxa, while MOs respond to and act on pathogenic taxa primarily through antiadhesive methods. Further research is needed to confirm the potential mechanisms driving these correlations. IMPORTANCE Bovine milk can harbor microbes that cause mastitis, milk spoilage, and foodborne illness. Fatty acids found in milk can be antimicrobial and milk oligosaccharides can have antiadhesive, prebiotic, and immune-modulatory effects. Relationships among milk microbes, fatty acids, oligosaccharides, and inflammation have been reported for humans. To our knowledge, associations among the milk microbial composition, fatty acids, oligosaccharides, and lactose have not been reported for healthy lactating cows. Identifying these potential relationships in bovine milk will inform future efforts to characterize direct and indirect interactions of the milk components with the milk microbiota. Since many milk components are associated with herd management practices, determining if these milk components impact milk microbes may provide valuable information for dairy cow management and breeding practices aimed at minimizing harmful and spoilage-causing microbes in raw milk.
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Affiliation(s)
- Laurynne C. Coates
- U.S. Department of Agriculture—Agricultural Research Service, Western Human Nutrition Research Center, Davis, California, USA
| | - Sierra D. Durham
- University of California, Davis, Food Science and Technology, Davis, California, USA
| | - David H. Storms
- U.S. Department of Agriculture—Agricultural Research Service, Western Human Nutrition Research Center, Davis, California, USA
| | - Andrew D. Magnuson
- U.S. Department of Agriculture—Agricultural Research Service, Grand Forks Human Nutrition Research Center, Grand Forks, North Dakota, USA
| | - Diane L. Van Hekken
- U.S. Department of Agriculture—Agricultural Research Service, Dairy and Functional Foods Research, Wyndmoor, Pennsylvania, USA
| | - Benjamin M. Plumier
- U.S. Department of Agriculture—Agricultural Research Service, Dairy and Functional Foods Research, Wyndmoor, Pennsylvania, USA
| | - John W. Finley
- U.S. Department of Agriculture—Agricultural Research Service, George Washington Carver Center, Beltsville, Maryland, USA
| | - Naomi K. Fukagawa
- U.S. Department of Agriculture—Agricultural Research Service, Beltsville Human Nutrition Research Center, Beltsville, Maryland, USA
| | - Peggy M. Tomasula
- U.S. Department of Agriculture—Agricultural Research Service, Dairy and Functional Foods Research, Wyndmoor, Pennsylvania, USA
| | - Danielle G. Lemay
- U.S. Department of Agriculture—Agricultural Research Service, Western Human Nutrition Research Center, Davis, California, USA
| | - Matthew J. Picklo
- U.S. Department of Agriculture—Agricultural Research Service, Grand Forks Human Nutrition Research Center, Grand Forks, North Dakota, USA
| | - Daniela Barile
- University of California, Davis, Food Science and Technology, Davis, California, USA
| | - Kenneth F. Kalscheur
- U.S. Department of Agriculture—Agricultural Research Service, U.S. Dairy Forage Research Center, Madison, Wisconsin, USA
| | - Mary E. Kable
- U.S. Department of Agriculture—Agricultural Research Service, Western Human Nutrition Research Center, Davis, California, USA
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8
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Stinson LF, George AD. Human Milk Lipids and Small Metabolites: Maternal and Microbial Origins. Metabolites 2023; 13:metabo13030422. [PMID: 36984862 PMCID: PMC10054125 DOI: 10.3390/metabo13030422] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/05/2023] [Accepted: 03/10/2023] [Indexed: 03/16/2023] Open
Abstract
Although there has been limited application in the field to date, human milk omics research continues to gain traction. Human milk lipidomics and metabolomics research is particularly important, given the significance of milk lipids and metabolites for infant health. For researchers conducting compositional milk analyses, it is important to consider the origins of these compounds. The current review aims to provide a summary of the existing evidence on the sources of human milk lipids and small metabolites. Here, we describe five major sources of milk lipids and metabolites: de novo synthesis from mammary cells, production by the milk microbiota, dietary consumption, release from non-mammary tissue, and production by the gut microbiota. We synthesize the literature to provide evidence and understanding of these pathways in the context of mammary gland biology. We recommend future research focus areas to elucidate milk lipid and small metabolite synthesis and transport pathways. Better understanding of the origins of human milk lipids and metabolites is important to improve translation of milk omics research, particularly regarding the modulation of these important milk components to improve infant health outcomes.
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Affiliation(s)
- Lisa F. Stinson
- School of Molecular Sciences, The University of Western Australia, Perth 6009, Australia
| | - Alexandra D. George
- Metabolomics Laboratory, Baker Heart and Diabetes Institute, Melbourne 3004, Australia
- Correspondence:
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9
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Effect of in vitro cultivation on human gut microbiota composition using 16S rDNA amplicon sequencing and metabolomics approach. Sci Rep 2023; 13:3026. [PMID: 36810418 PMCID: PMC9945476 DOI: 10.1038/s41598-023-29637-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/08/2023] [Indexed: 02/23/2023] Open
Abstract
Gut microbiota (GM) plays many key functions and helps maintain the host's health. Consequently, the development of GM cultivation under in vitro stimulating physiological conditions has gained extreme interest in different fields. In this study, we evaluated the impact of four culture media: Gut Microbiota Medium (GMM), Schaedler Broth (SM), Fermentation Medium (FM), and Carbohydrate Free Basal Medium (CFBM) on preserving the biodiversity and metabolic activity of human GM in batch in vitro cultures using PMA treatment coupled with 16S rDNA sequencing (PMA-seq) and LC-HR-MS/MS untargeted metabolomics supplemented with GC-MS SCFA profiling. Before the experiments, we determined the possibility of using the pooled faecal samples (MIX) from healthy donors (n = 15) as inoculum to reduce the number of variables and ensure the reproducibility of in vitro cultivation tests. Results showed the suitability of pooling faecal samples for in vitro cultivation study. Non-cultured MIX inoculum was characterized by higher α-diversity (Shannon effective count, and Effective microbial richness) compared to inocula from individual donors. After 24 h of cultivation, a significant effect of culture media composition on GM taxonomic and metabolomic profiles was observed. The SM and GMM had the highest α-diversity (Shannon effective count). The highest number of core ASVs (125) shared with non-cultured MIX inoculum and total SCFAs production was observed in the SM. These results might contribute to the development of standardized protocols for human GM in vitro cultivation by preventing methodological bias in the data.
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10
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Stinson LF, Ma J, Sindi AS, Geddes DT. Methodological approaches for studying the human milk microbiome. Nutr Rev 2022; 81:705-715. [PMID: 36130405 DOI: 10.1093/nutrit/nuac082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human milk contains a low-biomass, low-diversity microbiome, consisting largely of bacteria. This community is of great research interest in the context of infant health and maternal and mammary health. However, this sample type presents many unique methodological challenges. In particular, there are numerous technical considerations relating to sample collection and storage, DNA extraction and sequencing, viability, and contamination. Failure to properly address these challenges may lead to distortion of bacterial DNA profiles generated from human milk samples, ultimately leading to spurious conclusions. Here, these technical challenges are discussed, and various methodological approaches used to address them are analyzed. Data were collected from studies in which a breadth of methodological approaches were used, and recommendations for robust and reproducible analysis of the human milk microbiome are proposed. Such methods will ensure high-quality data are produced in this field, ultimately supporting better research outcomes for mothers and infants.
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Affiliation(s)
- Lisa F Stinson
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | - Jie Ma
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | - Azhar S Sindi
- Division of Obstetrics and Gynaecology, School of Medicine, The University of Western Australia, Perth, Australia.,is with the College of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Donna T Geddes
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
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11
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Ahuja JKC, Casavale KO, Li Y, Hopperton KE, Chakrabarti S, Hines EP, Brooks SPJ, Bondy GS, MacFarlane AJ, Weiler HA, Wu X, Borghese MM, Ahluwalia N, Cheung W, Vargas AJ, Arteaga S, Lombo T, Fisher MM, Hayward D, Pehrsson PR. Perspective: Human Milk Composition and Related Data for National Health and Nutrition Monitoring and Related Research. Adv Nutr 2022; 13:2098-2114. [PMID: 36084013 PMCID: PMC9776678 DOI: 10.1093/advances/nmac099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 04/18/2022] [Accepted: 09/07/2022] [Indexed: 01/28/2023] Open
Abstract
National health and nutrition monitoring is an important federal effort in the United States and Canada, and the basis for many of their nutrition and health policies. Understanding of child exposures through human milk (HM) remains out of reach due to lack of current and representative data on HM's composition and intake volume. This article provides an overview of the current national health and nutrition monitoring activities for HM-fed children, HM composition (HMC) and volume data used for exposure assessment, categories of potential measures in HM, and associated variability factors. In this Perspective, we advocate for a framework for collection and reporting of HMC data for national health and nutrition monitoring and programmatic needs, including a shared vision for a publicly available Human Milk Composition Data Repository (HMCD-R) to include essential metadata associated with HMC. HMCD-R can provide a central, integrated platform for researchers and public health officials for compiling, evaluating, and sharing HMC data. The compiled compositional and metadata in HMCD-R would provide pertinent measures of central tendency and variability and allow use of modeling techniques to approximate compositional profiles for subgroups, providing more accurate exposure assessments for purposes of monitoring and surveillance. HMC and related metadata could facilitate understanding the complexity and variability of HM composition, provide crucial data for assessment of infant and maternal nutritional needs, and inform public health policies, food and nutrition programs, and clinical practice guidelines.
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Affiliation(s)
- Jaspreet K C Ahuja
- Methods and Application of Food Composition Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Services, US Department of Agriculture, Beltsville, Maryland, USA.
| | - Kellie O Casavale
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, US Department of Health and Human Services, College Park, Maryland, USA
| | - Ying Li
- Methods and Application of Food Composition Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Services, US Department of Agriculture, Beltsville, Maryland, USA
| | - Kathryn E Hopperton
- Nutrition Premarket Assessment Division, Bureau of Nutritional Sciences, Food Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Subhadeep Chakrabarti
- Nutrition Premarket Assessment Division, Bureau of Nutritional Sciences, Food Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Erin P Hines
- Reproductive and Developmental Toxicology Branch, Public Health and Integrated Toxicology Division, US Environmental Protection Agency, Chapel Hill, North Carolina, USA
| | - Stephen P J Brooks
- Nutrition Research Division, Bureau of Nutritional Sciences, Food Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Genevieve S Bondy
- Bureau of Chemical Safety, Food Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Amanda J MacFarlane
- Nutrition Research Division, Bureau of Nutritional Sciences, Food Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Hope A Weiler
- Nutrition Research Division, Bureau of Nutritional Sciences, Food Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Xianli Wu
- Methods and Application of Food Composition Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Services, US Department of Agriculture, Beltsville, Maryland, USA
| | - Michael M Borghese
- Environmental Health Sciences and Research Bureau, Health Canada, Ottawa, Ontario, Canada
| | - Namanjeet Ahluwalia
- National Center for Health Statistics, Centers for Disease Control and Prevention, Department of Health and Human Services, Hyattsville, Maryland, USA
| | - Winnie Cheung
- Nutrition Premarket Assessment Division, Bureau of Nutritional Sciences, Food Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Ashley J Vargas
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Sonia Arteaga
- Environmental influences on Child Health Outcomes (ECHO) Program, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Tania Lombo
- Maternal Adolescent Pediatric Research Branch, Prevention Science Program, Division of AIDS, National Institute of Allergy and Infectious Diseases (NIAID), Bethesda, Maryland, USA
| | - Mandy M Fisher
- Environmental Health Sciences and Research Bureau, Health Canada, Ottawa, Ontario, Canada
| | - Deborah Hayward
- Nutrition Premarket Assessment Division, Bureau of Nutritional Sciences, Food Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Pamela R Pehrsson
- Methods and Application of Food Composition Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Services, US Department of Agriculture, Beltsville, Maryland, USA
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